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- EMDB-38430: Structure of the TOM40 complex with pre-protein -

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Basic information

Entry
Database: EMDB / ID: EMD-38430
TitleStructure of the TOM40 complex with pre-protein
Map data
Sample
  • Complex: TOM40 complex with pre-protein
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
KeywordsMitochondrial precursor protein translocase / Mitochondrial pre-protein transporte / Protein complex / mitochondrial outer membrane protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport ...mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol
Similarity search - Function
Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family ...Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit TOM6 / Mitochondrial import receptor subunit TOM22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit TOM5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYang LY / Shen QT
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the TOM40 complex with pre-protein
Authors: Yang LY / Shen QT
History
DepositionDec 25, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38430.png

Downloads & links

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Map

FileDownload / File: emd_38430.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0176
Minimum - Maximum-0.12573697 - 0.16624106
Average (Standard dev.)0.0003463394 (±0.0032060652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38430_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38430_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TOM40 complex with pre-protein

EntireName: TOM40 complex with pre-protein
Components
  • Complex: TOM40 complex with pre-protein
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
    • Protein or peptide: Mitochondrial import receptor subunit TOM40

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Supramolecule #1: TOM40 complex with pre-protein

SupramoleculeName: TOM40 complex with pre-protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499

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Macromolecule #1: Mitochondrial import receptor subunit TOM22

MacromoleculeName: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499
Molecular weightTheoretical: 19.194943 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MVELTEIKDD VVQLDEPQFS RNQAIVEEKA SATNNDVVDD EDDSDSDFED EFDENETLLD RIVALKDIVP PGKRQTISNF FGFTSSFVR NAFTKSGNLA WTLTTTALLL GVPLSLSILA EQQLIEMEKT FDLQSDANNI LAQGEKDAAA TANRTLQVDG S PGHHHHHH HHHH

UniProtKB: Mitochondrial import receptor subunit TOM22

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Macromolecule #2: Mitochondrial import receptor subunit TOM5

MacromoleculeName: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499
Molecular weightTheoretical: 5.993924 KDa
SequenceString:
MFGLPQQEVS EEEKRAHQEQ TEKTLKQAAY VAAFLWVSPM IWHLVKKQWK

UniProtKB: Mitochondrial import receptor subunit TOM5

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Macromolecule #3: Mitochondrial import receptor subunit TOM6

MacromoleculeName: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499
Molecular weightTheoretical: 6.41046 KDa
SequenceString:
MDGMFAMPGA AAGAASPQQP KSRFQAFKES PLYTIALNGA FFVAGVAFIQ SPLMDMLAPQ L

UniProtKB: Mitochondrial import receptor subunit TOM6

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Macromolecule #4: Mitochondrial import receptor subunit TOM7

MacromoleculeName: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499
Molecular weightTheoretical: 6.876955 KDa
SequenceString:
MSFLPSFILS DESKERISKI LTLTHNVAHY GWIPFVLYLG WAHTSNRPNF LNLLSPLPSV

UniProtKB: Mitochondrial import receptor subunit TOM7

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Macromolecule #5: Mitochondrial import receptor subunit TOM40

MacromoleculeName: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499
Molecular weightTheoretical: 42.071141 KDa
SequenceString: MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE ...String:
MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE QDYQASDFSV NVKTLNPSFS EKGEFTGVAV ASFLQSVTPQ LALGLETLYS RTDGSAPGDA GVSYLTRYVS KK QDWIFSG QLQANGALIA SLWRKVAQNV EAGIETTLQA GMVPITDPLM GTPIGIQPTV EGSTTIGAKY EYRQSVYRGT LDS NGKVAC FLERKVLPTL SVLFCGEIDH FKNDTKIGCG LQFETAGNQE LLMLQQGLDA DGNPLQALPQ L

UniProtKB: Mitochondrial import receptor subunit TOM40

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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